Genetic diversity analysis and subspecies classification of Thailand rice landraces using DNA markers

Abstract

Genetic diversity among 126 rice accessions, including 110 Thai landraces and 16 varieties used as subspecies reference, were evaluated by three types of DNA markers, InDel (Insertion/Deletion), inter-simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers. Twelve InDel primer pairs, based on DNA sequence polymorphism between ‘93-11’ ( indica ) and ‘Nipponbare’ ( japonica ), were used to identify subspecies of landraces. Most of the local rice samples had either ‘93-11’ alleles or ‘Nipponbare’ alleles. The scatter plotting of the principal component analysis (PCA) and dendrogram results based on InDel data could clearly classify landraces into two groups, indica and japonica . InDel and SSR markers showed the average polymorphic information content (PIC) values of 0.3707 and 0.6367, respectively. The dendrogram, based on combining InDel, ISSR and SSR data, could classify rice samples into five clusters at a cut-off genetic similarity value of about 0.70. The genetic similarity within landraces was low, indicating that Thai local rice samples have a great genetic diversity. The results of this experiment provide helpful data for rice germplasm management in breeding program. Key word: Rice, genetic diversity, DNA markers, simple sequence repeat (SSR), inter-simple sequence repeat (ISSR), insertion/deletion (InDel).